Variant report

Variant	rs2241718
Chromosome Location	chr19:41829606-41829607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41828482..41836150-chr19:41836490..41842395,12	K562	blood:
2	chr19:41826823..41830968-chr19:41831922..41834042,4	K562	blood:
3	chr19:41767636..41772705-chr19:41827976..41830874,5	K562	blood:
4	chr19:41821189..41824039-chr19:41826906..41830511,3	MCF-7	breast:
5	chr19:41828559..41831020-chr19:41944641..41946935,2	MCF-7	breast:
6	chr19:41814818..41818108-chr19:41828444..41830953,5	K562	blood:
7	chr19:41829468..41831265-chr19:41933242..41935169,2	MCF-7	breast:
8	chr19:41813217..41816431-chr19:41827201..41830694,5	MCF-7	breast:
9	chr19:41827333..41835079-chr19:41855373..41860241,10	K562	blood:
10	chr19:41827408..41831164-chr19:41901595..41905295,3	MCF-7	breast:
11	chr19:41825498..41830119-chr19:41857290..41861615,7	MCF-7	breast:
12	chr19:41825452..41832651-chr19:41855170..41863054,16	K562	blood:
13	chr19:41824762..41827482-chr19:41828175..41830071,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000077348	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000142046	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10410836	0.85[EUR][1000 genomes]
rs10421990	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs1056854	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11466345	0.81[JPT][hapmap]
rs11466347	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11466359	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11879429	0.85[ASN][1000 genomes]
rs11879435	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11879562	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs11880564	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880729	0.85[ASN][1000 genomes]
rs11881940	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11881953	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12327659	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs12972266	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12972949	0.90[ASN][1000 genomes]
rs12974323	0.85[EUR][1000 genomes]
rs12974420	0.84[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12976536	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12977563	0.85[ASN][1000 genomes]
rs12980267	0.89[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12980298	0.85[EUR][1000 genomes]
rs12980480	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs12980942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12981053	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12983047	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12983339	0.86[ASN][1000 genomes]
rs12984160	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12985162	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12985339	0.91[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958994	0.94[EUR][1000 genomes]
rs16958996	0.94[EUR][1000 genomes]
rs16958999	0.94[EUR][1000 genomes]
rs1865051	1.00[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs1865052	0.94[EUR][1000 genomes]
rs1865053	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs1946612	0.89[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1946613	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2053086	0.84[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241719	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304230	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2304231	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2304232	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34075897	0.97[EUR][1000 genomes]
rs34322801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34945449	0.94[EUR][1000 genomes]
rs35501756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35812313	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3745295	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs3752705	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs3760659	0.89[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3760660	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3816052	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs3826714	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4456618	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4591267	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs61459202	0.97[ASN][1000 genomes]
rs66724427	0.85[EUR][1000 genomes]
rs67511749	0.93[EUR][1000 genomes]
rs67744888	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6957	1.00[CEU][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs7245398	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7248164	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7250883	0.89[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7254679	0.82[CEU][hapmap]
rs7256416	0.85[EUR][1000 genomes]
rs7256856	0.85[EUR][1000 genomes]
rs7257310	1.00[CEU][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs7257742	0.97[EUR][1000 genomes]
rs7257825	0.85[EUR][1000 genomes]
rs7258749	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs8103839	0.84[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8105161	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8105901	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8109167	1.00[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911769	chr19:41813676-41845801	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2241718	BAX	cis	cerebellum	SCAN
rs2241718	FLT3LG	cis	cerebellum	SCAN
rs2241718	PLEKHA4	cis	cerebellum	SCAN
rs2241718	TSKS	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41818200-41831600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:41818400-41831200	Strong transcription	Thymus	Thymus
3	chr19:41818600-41854800	Strong transcription	Dnd41	blood
4	chr19:41819000-41830600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:41821400-41830400	Strong transcription	Fetal Brain Female	brain
6	chr19:41821600-41830000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr19:41822000-41830600	Strong transcription	Primary T cells from cord blood	blood
8	chr19:41822400-41831000	Weak transcription	Psoas Muscle	Psoas
9	chr19:41823200-41830600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:41823200-41832000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:41823400-41830400	Weak transcription	Fetal Kidney	kidney
12	chr19:41823400-41830800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:41823400-41832200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:41824200-41830400	Strong transcription	Brain Germinal Matrix	brain
15	chr19:41824400-41830000	Genic enhancers	Placenta	Placenta
16	chr19:41824400-41830600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:41824400-41834000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:41824600-41830800	Genic enhancers	Spleen	Spleen
19	chr19:41825000-41830600	Genic enhancers	Right Ventricle	heart
20	chr19:41825600-41829800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr19:41826800-41829800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:41827000-41830200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
23	chr19:41827000-41830400	Genic enhancers	Fetal Muscle Trunk	muscle
24	chr19:41827000-41830600	Genic enhancers	Fetal Muscle Leg	muscle
25	chr19:41827000-41830800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:41827000-41832800	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr19:41827200-41830000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:41827200-41830000	Genic enhancers	Colonic Mucosa	Colon
29	chr19:41827200-41830000	Genic enhancers	Lung	lung
30	chr19:41827200-41830400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr19:41827200-41830600	Enhancers	Right Atrium	heart
32	chr19:41827200-41832000	Enhancers	NHDF-Ad	bronchial
33	chr19:41827400-41830600	Genic enhancers	Primary B cells from peripheral blood	blood
34	chr19:41827400-41830600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
35	chr19:41827400-41830800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:41827400-41831000	Enhancers	Ovary	ovary
37	chr19:41827400-41831000	Flanking Active TSS	HepG2	liver
38	chr19:41827400-41831200	Weak transcription	Aorta	Aorta
39	chr19:41827400-41831200	Enhancers	Left Ventricle	heart
40	chr19:41827400-41833000	Enhancers	Primary hematopoietic stem cells	blood
41	chr19:41827400-41833000	Genic enhancers	Fetal Thymus	thymus
42	chr19:41827600-41830600	Genic enhancers	Fetal Stomach	stomach
43	chr19:41827600-41831800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr19:41827800-41830400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr19:41827800-41830600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:41827800-41830600	Weak transcription	Brain Angular Gyrus	brain
47	chr19:41827800-41830800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr19:41827800-41832200	Enhancers	Stomach Mucosa	stomach
49	chr19:41828000-41830000	Weak transcription	GM12878-XiMat	blood
50	chr19:41828000-41830200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links